What method did you use to obtain root?
Have you verified root with any other apps?
You haven't hidden root by any chance, for instance in an attempt to make ISIS work?
---------- Post added at 08:50 AM ---------- Previous post was at 08:45 AM ----------
One thing does come to mind, based on experience on one of my past devices:
I was having trouble getting Busybox to install on my old HTC Flyer. It was properly rooted, and couldn't find what else could be wrong.
I was trying the Stericson installer from the Play store (which is what I had usually one); but using the installer from JRummy did the trick.
Couldn't find any rhyme of reason for this, it just worked.
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Phone: AT&T HTC One (M8)
Tablet: Samsung Galaxy Tab Pro 8.4 (WiFi only)